The business magazine, which released the list Wednesday, ranks each city based on the number of firms listed on its ranking of the 5,000 fastest-growing companies. The businesses are ranked based on the past three years of revenue growth.

New York City topped the list, with 205 of the nation's fastest-growing companies, many of them rooted in the Big Apple's booming tech scene. San Diego, with 81 companies on the list, ranked between fourth-place Austin (87 firms) and sixth-place Houston (76 firms). The top-cities ranking only counted firms in the San Diego city limits. Countywide, the number of firms on the Inc. 5000 was 113.

Inc.'s 2014 Top 10 Cities for Fast-Growth Companies

New York

Chicago

Atlanta

Austin

San Diego

Houston

San Francisco

Dallas

Irvine

Denver

"It's not the first time San Diego shines," said Inc. 5000 editor Diana Ransom. "It has always punched in higher than the size of its metro area would suggest."

San Diego didn't make the 2012 top-cities ranking, but in 2013 it landed in seventh place with 71 companies on the Inc. 5000, behind Houston and San Francisco.

"This is a very valuable finding for San Diego," said Lynn Reaser, chief economist for Point Loma Nazarene University. "Having an outside source validating your ranking and your potential for growth is very compelling. Plus, I think it defies much of the negative publicity that the public seems to be digesting almost on a daily basis: The perception that companies are leaving in a mass exodus."

San Diego's enviable weather has helped make it a hotbed of innovation and growth for companies like utility metering and billing firm Multifamily Utility, Inc. writer Yolanda Lu wrote. Multifamily, San Diego's fastest-growing company on the Inc. 5000, experienced a 5,196 percent surge in revenue over the last three years, from $108,707 in 2010 to $5.7 million in 2013, landing it in 56th place nationwide. Photo archiving company PhotoBin, in 60th place, saw revenue grow from $125,117 in 2010 to $6.3 million in 2013, an increase of 5,003 percent.

"Overall, we like this list in a lot of ways," said Mark Cafferty, CEO of the San Diego Regional Economic Development Corporation. "It's really based on growth, and I think San Diego's story is one of growth."